Documenting and cleaning #15

* Remove unused/commented code fragments
* Remove unused fields
* Improve/add Javadoc (especially links to methods and classes)
* Suppress warnings on non-used methods in STK500v1, where these
  were not needed for Optiboot communications, but could be used with
  a proper programmer; convert most of these to TODO annotations
* Refactor out triggerSwitch in Reader (use switchState instead)